VMD-L Mailing List

From: Thomas Evangelidis (te8624_at_mbg.duth.gr)
Date: Fri Jul 17 2009 - 03:30:45 CDT

Try to combine "within" atomselections with interatomic distance
measurements, that will alleviate the burden of VMD. I used this
approach when measuring the N closest waters to a protein ;)

~Tom

>
> Bin,
> The "within" commands in VMD use a spatial decomposition to
> accelerate the search. You can find the related code in
> SpatialSearch.[Ch] in the VMD source tree.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Jul 16, 2009 at 09:29:43AM -0700, BIN ZHANG wrote:
>> Dear all:
>>
>> Can someone tell me or point me a reference about the algorithm used
>> to implement *within* command in VMD? I'm trying to do similar thing
>> by calculating the distance between all atom-pairs, which is really
>> really slow...
>>
>> Thanks,
>>
>> Bin
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>

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